Journal article
Impact of regulatory variation across human iPSCs and differentiated cells
NE Banovich, YI Li, A Raj, MC Ward, P Greenside, D Calderon, PY Tung, JE Burnett, M Myrthil, SM Thomas, CK Burrows, IG Romero, BJ Pavlovic, A Kundaje, JK Pritchard, Y Gilad
Genome Research | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2018
Abstract
Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility, and DNA methylation. Our analysis focused on a comp..
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Awarded by National Institutes of Health
Funding Acknowledgements
We thank members of the Pritchard and Gilad Labs for helpful discussions. We also thank the reviewers for their valuable comments and suggestions. This work was supported by NIH grants GM007197, AG 044948, MH084703, MH101825, HG007036, CA149145, and HL092206; by a Center for Computational, Evolutionary and Human Genomics Fellowship; by an EMBO Long-Term Fellowship (ALTF 751-2014) and Marie Curie Actions; and by the Howard Hughes Medical Institute.